All this is prob. true, but I repeat -
should tight default stereochemistry be a requirement at the early
stages of refinement at reso > 2.5A anyay?
Eleanor
Anthony Duff wrote:
In my opinion...
CNS seems superior for low resolution structures (resolution worse
than 3A) and early refinement (R worse than 30%). Reasons:
* good radius of convergence,
* tight default stereochemistry,
* very easy to use with a simple model
* simulated annealing
* ability to refine part only of the model
* ability to use harmonic restraints,
* ability to not refine B-factors,
* ability to only refine B-factors
Otherwise REFMAC is superior:
* more aggressive minimisation algorithm.
* very easy to use alternate conformers
* Ongoing development
* excellent community support for when things get tricky (ccp4bb)
I suggest that the best transition point is where you need to model
alternate conformers. Once you have your first alternate conformer,
abandon CNS and use REFMAC from that point forward.
Anthony
At 08:57 AM 7/12/2005, you wrote:
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Dear all,
My model (total 354 residues) has 13 residues which have alternate
conformations. when I generate the alternate conformation with
alternate.inp in CNS, the program does not give me the AC conformers
because the atom selection only allows for 265 letter. However, all
these residue selection will more than 264 strings. Does any one know
how to the alternates in CNS?
DEFINE>{========================== atom selection
===========================}
DEFINE>
DEFINE>{* select atoms to have multiple conformations *}
%COPYST-ERR: ST2MAX too small. Check input file.
Offending string:"{===>} atom_select=((segid A and residue
12) or (segid A and residue 169) or (segid A and residue 175) or
(segid A and residue 172) or (segid A and residue 37) or (segid A and
residue 222) or (segid A and residue 126) or (segid A and residue 51)
or (segid A and re "
with length= 265
Max allowed length of string= 264
----------------------------------------------------------------------
Anthony Duff
Postdoctoral Fellow
School of Molecular and Microbial Biosciences
Biochemistry Building, G08
University of Sydney, NSW 2006 Australia
Phone. 61-2-9351-3907 Fax. 61-2-9351-4726
----------------------------------------------------------------------
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tel;work:+44 (0) 1904 328259
tel;fax:+44 (0) 1904 328266
tel;home:+44 (0) 1904 424449
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